MtoZ Biolabs provides 4D Label-free Quantitative Proteomics Analysis Service using high-resolution LC-MS/MS with ion mobility to deliver deep and accurate protein quantification without labeling. This service supports discovery research, biomarker screening, and mechanism studies across a wide range of cells, tissues, and biofluids.
What Is 4D Label-free Quantitative Proteomics?
Label-free quantitative proteomics compares protein expression between samples based on mass spectrometry signal intensity or spectral information, without using isotopic or chemical labels. It is widely used for differential proteome analysis because it is flexible in experimental design and compatible with clinical or precious samples.
4D label free quantitative proteomics builds on this concept by introducing an additional ion mobility dimension on the timsTOF Pro platform. Using a data dependent acquisition–parallel accumulation serial fragmentation (ddaPASEF) scanning mode, 4D label free proteomics synchronizes ion accumulation and fragmentation in the trapped ion mobility cell, improving ion utilization, sensitivity, and acquisition speed. By integrating DDA with PASEF and separating ions according to their collision cross section (CCS), the system resolves peptides in four dimensions: retention time, m/z, intensity, and ion mobility.
This 4D strategy helps to
🔸Reduce interference from co eluting peptides in complex samples
🔸Improve signal to noise ratios for low abundance proteins
🔸Distinguish peptides with similar m/z but different sizes or conformations through CCS based separation
🔸Increase identification confidence and quantitative robustness across large sample sets
As a result, 4D label-free proteomics provides deeper proteome coverage, better separation of overlapping signals, and more reliable quantitative data for downstream biological interpretation.
Jiang, H. et al. BMC Pregnancy and Childbirth, 2024.
Figure 1. Detection Flow of 4D Label-free Proteomics
4D Label-free Quantitative Proteomics Analysis Service at MtoZ Biolabs
Based on the timsTOF Pro 2 and timsTOF HT platforms combined with TIMS technology, MtoZ Biolabs provides 4D Label-free Quantitative Proteomics Analysis Service with high sensitivity and high resolution. You only need to submit your samples (such as cells, tissues, or biofluids), and we handle the entire workflow, including protein extraction, enzymatic digestion, peptide separation, 4D LC-MS/MS acquisition, raw data processing, quantitative analysis, and downstream bioinformatics interpretation.
Why Choose MtoZ Biolabs
✔️Deeper Proteome Coverage
Ion mobility based 4D separation improves resolution of co-eluting peptides and enhances overall protein identification.
✔️Improved Quantitative Accuracy
Cleaner separation and reduced interference support more reliable label-free quantification, particularly for low-abundance proteins.
✔️Flexible Experimental Design
Easy to scale from small pilot projects to large cohorts and complex multi-group or time series studies.
✔️High Throughput and Robust QC
Standardized workflows, internal standards, and QC samples ensure reproducible performance across runs and batches.
✔️Expert Scientific Support
Proteomics specialists assist with study design, sample planning, and interpretation of 4D label-free data in a biological context.
Applications of 4D Label-free Quantitative Proteomics Analysis Service
4D Label-free Quantitative Proteomics Analysis Service can be applied to many research scenarios.
1. Biomarker Discovery and Prioritization
Identify proteins that differ between disease and control groups, or responders and non-responders, with improved sensitivity and depth.
2. Mechanism of Action and Pathway Analysis
Characterize proteomic changes following drug treatment, gene perturbation, or environmental stress, and link them to pathways and networks.
3. Signaling and Regulatory Protein Profiling
Improve detection of low-abundance kinases, transcription regulators, and other signaling components through 4D separation.
4. Time Course and Dynamic Studies
Track temporal protein expression patterns during development, differentiation, or therapeutic intervention.
FAQ
Q1: What types of samples are suitable?
We accept a wide range of samples, including:
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Cell pellets from adherent or suspension cell lines
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Primary cells from blood, tissues, or organoids
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Fresh frozen tissues or biopsies
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Biofluids such as serum, plasma, CSF, urine, and others
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Microbial cultures or model organism samples
For unusual sample types or low-yield materials, please contact MtoZ Biolabs for customized preparation guidance.
Q2: How should I prepare my samples?
1. Use clean, low binding tubes and avoid repeated freeze thaw cycles
2. Snap freeze samples after collection and store at −80 °C
3. Avoid strong detergents, very high salt, and large amounts of reducing agents
4. Record detailed metadata (sample type, group, treatment, time point)
5. Ship on dry ice with a clearly labeled sample list
Detailed requirements and recommendations can be found in the Sample Submission Guidelines for Proteomics.
Q3: What is the service general workflow?
Q4: What data formats are provided?
1. Raw LC-MS/MS files in instrument specific formats
2. Peptide and protein identification and quantification tables in .xlsx or .csv
3. Statistical and functional analysis outputs in .xlsx or .csv
4. Publication ready figures in high resolution .png or .tiff
5. A concise PDF report summarizing methods, QC metrics, and key findings
6. Additional formats can be provided on request
Start Your Project with MtoZ Biolabs
MtoZ Biolabs' 4D Label-free Quantitative Proteomics Analysis Service is designed to provide more rapid, high-throughput, and cost-effective analysis, with exceptional data quality and minimal sample consumption. Free project evaluation, welcome to learn more details.
